Past and Ongoing Research Projects


Numbers preceeding the publications refer to the chronological order present on Nickrent's publication list HERE.

1. Biology of Philippine Rafflesia species

Rafflesia verrucosa The Philippine tropical rainforests are among the World’s Biodiversity Hotspots but are threatened by human activities. They are home to the holoparasitic Rafflesia, famous for possessing the largest single flower in the world.  Until 2002, only two species of Philippine Rafflesia were known, but following a number of investigations ten endemic species are now recognized.  One of the most unusual of all Rafflesia species is the most recently described, R. verrucosa (shown at left). This species has the smallest average flower diameter of any in the genus and also has an assemblage of unusual and unique morphological features.

A grant from the National Geographic Society allowed several collecting trips to the Philippines for myself as well as my collaborators Julie Barcelona and Pieter Pelser, both University of Canterbury, Christchurch NZ, and Benjamin Van Ee (currently University of Puerto Rico, Mayagüez). For the phylogenetic and population genetic studies, we have already obtained samples for DNA analysis of Rafflesia and its host plants Tetrastigma (Vitaceae).  This systematic data will provide the baseline information needed to address a number of issues relating to speciation, host relationships, biogeography and conservation.  Eleven of the 13 Philippine Rafflesia species have been obtained to date - currently missing R. aurantia and R. consueloae.
Publications:

125. Pelser, P.B, D. L. Nickrent, C. E. C Gemmill, and J. F. Barcelona. 2017. Genetic diversity and structure in the Philippine Rafflesia lagascae complex (Rafflesiaceae) inform its taxonomic delimitation and conservation. Systematic Botany 42(3): 543–553. For a PDF file of this article click HERE.
121. Pelser, P. B., D. L. Nickrent, & J. F. Barcelona. 2016. Untangling a vine and its parasite: Host specificity of Philippine Rafflesia (Rafflesiaceae). Taxon 65(4):739-758. For a PDF file of this article click HERE.  For Supplemental data, click HERE.
111. Pelser P.B., D. L. Nickrent, J. R. C. Callado, and J. F. Barcelona. 2013. Mt. Banahaw reveals: The resurrection and neotypification of the name Rafflesia lagascae (Rafflesiaceae) and clues to the dispersal of Rafflesia seeds. Phytotaxa 131: 35–40. For a PDF file of this article click HERE.
107. Barcelona, J. F., E. S. Fernando, D.  L. Nickrent, D. S. Balete, and P. B. Pelser.  2011. An amended description of Rafflesia leonardi and a revised key to Philippine Rafflesia (Rafflesiaceae). Phytotaxa 24: 11-18. For a PDF file of this article click HERE.
104
. Balete D. S., P. B. Pelser, D. L. Nickrent, and J. F. Barcelona. 2010. Rafflesia verrucosa (Rafflesiaceae), a new species of small-flowered Rafflesia from Mindanao, Philippines. Phytotaxa 10: 49-57. For a PDF file of this article click HERE.


2. Genomics of Philippine Rafflesia

DNA Sequence
Early in 2010, the idea of using Next Generation DNA sequencing on Rafflesia was being discussed by Nickrent, Geisler (SIUC) and Barcelona and Pelser (University of Canterbury). In October of 2010, Julie Barcelona traveled to the Philippines for fieldwork associated with the National Geographic Society grant, and was joined in November by Nickrent and Pelser.  With the help of professional contacts, fresh tissues of six Rafflesia species were obtained and processed. The laboratory facilities of Dr. Gisela Concepcion at The Marine Science Institute, University of the Philippines, Diliman were used for DNA and RNA extractions. This arrangement was facilitated by Dr. Michael Purugganan at New York University who is also Filipino.

Two species, R. lagascae (originally called R. manillana) and R. leonardi, were chosen for whole genome sequences (the others stored for later projects). Both 454 and Illumina sequencing runs were  conducted and these genomes were assembled by Matt Geisler. A paper was written (Nickrent and 8 coauthors) reporting the nearly complete mitochondrial genome of Rafflesia leonardi, as well as the complete loss of the chloroplast genome in this species. That paper was submitted to PLOS One September 2013 but was rejected. A revised manuscript was submitted to BMC Genomics December 2013 but it was also rejected. In the meanwhile, collaborators Purugganan and Molina conducted genomic analysis on another species, R. lagascae, using the Geisler assembly. This paper, reporting similar findings as the one on R. leonardi, was Advance Access published January 2014 in Molecular Biology & Evolution. A third attempt to publish the R. leonardi paper, incorporating the comments and suggestions from all previous reviews, was made in March 2015. This time, the paper was rejected by Genome Biology & Evolution because it was considered to similar to the R. lagascae paper. These data have still not been published.
Publications:

Molina J, et al.(16 other authors). 2014. Possible loss of the chloroplast genome in the parasitic flowering plant Rafflesia lagascae (Rafflesiaceae). Molecular Biology and Evolution 31:793-803.



3. Flora of the Philippines

Co's Digital Flora The Philippines is one of the world’s top 25 biodiversity hotspots. Unfortunately, the forests that harbor its remarkable biodiversity are in decline and this endangers the livelihoods of many Filipinos who depend on it for, food, water, and protection against climatic extremes, as well as ecotourism and aesthetic enjoyment. Efforts to mitigate this trend rely on knowledge of the organisms that compose these ecosystems, but a modern overview of the over 9,000 Philippine plant species is currently lacking. Leonardo L. Co was a world-renowned Philippine plant taxonomist who devoted much of his life to studying the plant diversity of this country. His "magnum opus" was a comprehensive checklist of Philippine plants, updating that of Merrill (1923). Sadly, Co’s life was tragically ended on 15 Nov. 2010. We obtained permission from Co’s family to make his unpublished plant checklist and his more than 10,000 plant photographs available on the website Co’s Digital Flora of the Philippines. This website, constructed by Nickrent, contains contributions from collaborators Barcelona, Pelser, and Molina as well as input from a number of specialists in particular plant groups. All of the Philippine plant photos reside on PhytoImages and are linked to the Co's Digital Flora of the Philippines site. At present we have assembled over 50,000  photographs of Philippine plants.  This is the most comprehensive web site available on the internet dealing with the Philippine flora. Our team received funding from the Rufford Small Grants for Nature Conservation program (UK) for a project entitled “Co’s Digital Flora of the Philippines: cybertaxonomy to the rescue of conservation”.  In the absence of a written Flora for the Philippines, our goal is to develop the Flora into a well-illustrated website that provides up-to-date taxonomic information and a comprehensive overview of Philippine vascular plants. By increasing the number of illustrated plant species, the team can develop the Flora into a one-of-a-kind taxonomic framework, boosting biodiversity and conservation research, management, and teaching.
Publications:

112. Barcelona J. F., D. L. Nickrent, J. V. LaFrankie, J. R. C. Callado and P. B. Pelser. 2013. Co's digital flora of the Philippines: plant identification and conservation through cybertaxonomy. Philippine Journal of Science 142: 57-67. For a PDF file of this article click HERE.

Website:

Co's Digital Flora of the Philippines

4. Photographic documentation and databases

PhytoImages logo The goal PhytoImages is to photographically document the flora of the world. It is part of the Diversity of Life project developed by Kevin Nixon (Cornell University) and collaborators who started the sister web site, PlantSystematics.orgPhytoImages began in April 2006, this server being purchased with funds placed into an account by the late Dr. Walter Welch.  In addition to over 1000 slides from Dr. Welch, the majority of digital images have come from the collections of Nickrent, Pieter Pelser and our most recent curatorial board member, Dr. Mihai Costea. As of November 2017 the site contains over 121,000 images and is growing rapidly. The value of this database is that these photos can be accessed and used in many different ways as illustrated by the following three web sites that utilize these photos:

Publications:

119. Pearse, I. S., G. Spyreas, D. Nickrent, P. Anders, A. Epstein, & M. Greenwood. 2015. Illinois Plants (www.inhs.illinois.edu/data/plantdb) is here: A new online resource for botanists and plant enthusiasts in Illinois. Illinois Natural History Survey Reports No. 413 (10): 19-20.3. For a PDF file of this article click HERE.

112. Barcelona J. F., D. L. Nickrent, J. V. LaFrankie, J. R. C. Callado and P. B. Pelser. 2013. Co's digital flora of the Philippines: plant identification and conservation through cybertaxonomy. Philippine Journal of Science 142: 57-67.
For a PDF file of this article click HERE.

Webpages
PhytoImages

5. Phylogenetics of Thesium and relatives

Thesium flower
With over 300 species, Thesium is the largest genus in Santalales. Worldwide in distribution, its highest diversity is in the Cape region of South Africa. Regional taxonomic works exist yet no modern comprehensive phylogenetic study is available. Several years ago I  began of collaboration with Dr. Miguel A. García (Real Jardín Botánico Madrid) to generate a molecular phylogeny of the genus.  Miguel had already been working on taxonomic aspects of tropical African Thesium and expanded his scope to include species of the genus from throughout its worldwide distribution.  Thesium samples from herbarium specimens as well living material were obtained, the latter particularly during field work in South Africa (2007).  Nuclear ribosomal ITS was sequenced for 294 taxa, 282 of which were from Thesium representing 165 names. A smaller number of taxa were sequenced for the chloroplast trnLF and trnDT regions. Some results that conflict with previous concepts include 1) no support for the segregation of "Chrysothesium" from Thesium, 2) the South American species (Section Psilothesium) are nested within the tropical African clade, and 3) the genera Kunkeliella and Thesidium are nested withing Thesium and thus should not be maintained as separate genera.

One Thesium species, T. lineatum, appeared as sister to the outgroup genus Osyridicarpos, not with other South African Thesium species. For this reason, and because of marked morphological differences, it was named as a new genus, Lacomucinaea, in honor of Ladislav "Laco" Mucina, an expert on the vegetation of southern Africa.
Publications:

116. Nickrent, D., & García, M. 2015. Lacomucinaea, a new monotypic genus in Thesiaceae (Santalales). Phytotaxa 224:173-184. For a PDF file of this article click HERE.

Nickrent, D. García, M, and Mucina, L. 2008. A phylogeny of Thesium (Santalaceae) using nuclear ribosomal ITS sequences. Abstract ID 239. Botany 2008, Vancouver, BC, July 26-30, 2008. Abstract available HERE.

6. Phylogenetics and taxonomy of Santalales

Santalales composite image

Santalales Tree
The first molecular phylogeny of the sandalwood order (Santalales) was published over 20 years ago (Nickrent and Franchina 1990) and since those humble beginnings my lab and collaborators have generated much information about the evolution of this fascinating order of plants. Some of the questions that our group has addressed include 1) how many times has parasitism evolved? 2) how many times has the mistletoe habit evolved? 3) are the polymorphic families Santalaceae and Olacaceae monophyletic? and 4) what are the relationships among the genera in the large family Loranthaceae?

Every group traditionally recognized as a family has been examined using molecular techniques.  This work was possible only through the collaborative efforts of these individuals: Olaceae (Dr. Valéry Malécot), Loranthaceae (Drs. Romina Vidal-Russell and Guillermo Amico), Misodendraceae (Dr. Vidal-Russell) and Santalaceae (Drs. Joshua Der and Miguel A. García).  The Taxon publication (Nickrent et al. 2010) provided a complete synopsis of current understanding of relationships in the order, and gave a revised classification based mainly on the molecular evidence.

During the course of this work, four new genera were named (Hondurodendron, Lacomucinaea, Pilgerina, and Staufferia).  The reclassification of the order based on the concept of monophyly resulted in some new (or recycled) family names.  Olacaceae was split into Aptandraceae, Coulaceae, Erythropalaceae, Octoknemaceae, Olacaceae s. s., Schoepfiaceae, Strombosiaceae, and Ximeniaceae.  Santalaceae was split into Amphorogynaceae, Cervantesiaceae, Comandraceae, Nanodeaceae, Santalaceae s. st.,  and Thesiaceae.  Three genera formerly classified in Santalaceae were moved to Schoepfiaceae (Arjona, Quinchamalium) and Opiliaceae (Anthobolus).  Excluding Balanophoraceae, the order now consists of 18 families, 148 genera and nearly 2300 species.  Our classification of Olacaceae was adopted by the Angiosperm Phylogeny Group (APG III 2009) but unfortunately they did not follow our recommendations for "Santalaceae s. lat." and chose to lump Viscaceae into it. My viewpoint on this was expressed in the Haustorium newsletter found on pp. 4-6 HERE.

Answers to some of the questions raised above can now be given. It appears that parasitism evolved just once in the order, although more recent multigene analyses draw this conclusion into question (stay tuned!).  It seems clear, however, that the mistletoe habit evolved five times independently. "Santalaceae" and "Olacaceae", as traditionally defined, were polyphyletic.  In our new classification all families are monophyletic.  Thanks to the efforts of Romina Vidal-Russell, we now have a phylogeny for Loranthaceae.  These results allowed us to proposed the first infrafamilial classification of the family based on phylogenetic evidence.  Nuytsia is sister to all other genera in the family and base chromosome number shows a progressive aneuploid reduction from X=12 in basal genera to X=9 in more derived clades (e.g. the African members).  These data literally turned a previous biogeographic concept on its head, highlighting dispersal, not vicariance, for the origin of the African and Asian loranths.
Publications:

126. Nickrent D. L. 2017. Status of the genera Colpoon, Osyris and Rhoiacarpos in South Africa. Bothalia: African Biodiversity & Conservation 47(1): (online 13 Nov. 2017).
For a PDF file of this article click HERE.
122. Nickrent, D. L. 2016. Ximeniaceae, Schoepfiaceae, Comandraceae, Thesiaceae, Cervantesiaceae, Santalaceae, Viscaceae.  Pp. 404-440 in: Flora North America, Volume 12, Flora North America Editorial Committee (eds.), Oxford University Press, New York.
For a PDF file of this article click HERE. These treatments are available online HERE.
118. Devkota, M. P., J. Macklin, &, D. L. Nickrent. 2015. The status of the mistletoe genus Dufrenoya Chatin (Amphorogynaceae) with a specific focus on Nepal. Flora 215:75-83.
For a PDF file of this article click HERE.
115. Su H.-J., J.-M. Hu, F. E. Anderson and D. L. Nickrent. 2015.  Phylogenetic relationships of Santalales with insights into the origins of holoparasitic Balanophoraceae. Taxon 64(3): 491-506. For a PDF file of this article click HERE.
106
. Nickrent, D. L. 2011. Santalales (Including Mistletoes). Encyclopedia of Life Science. John Wiley & Sons, Ltd.: Chichester [DOI: 10.1002/9780470015902.a0003714.pub2]. Wiley website (search for article) HERE. For a PDF file of this article click HERE.
103.  Ulloa, C. U, D. L. Nickrent , C. Whitefoord, and D. L. Kelly. Hondurodendron, a new monotypic genus of Aptandraceae from Honduras. Annals of the Missouri Botanical Garden 97: 457-467. For a PDF file of this article click HERE.
101. Nickrent, D. L. V. Malécot, R. Vidal-Russell, and J. P. Der. 2010. A revised classification of Santalales. Taxon 59: 538-558. For a PDF file of this article click HERE.  Supplemental data file on chromosome numbers HERE.
95. Vidal-Russell, R. and D. L. Nickrent. 2008. Evolutionary relationships in the showy mistletoe family (Loranthaceae). American Journal of Botany 95: 1015-1029. For a PDF file of this article click HERE.
93. Rogers, Z. S., D. L. Nickrent, and V. Malécot. 2008. Staufferia and Pilgerina: two new arborescent genera of Santalaceae from Madagascar. Annals of the Missouri Botanical Garden 95: 391-404. For a PDF file of this article click HERE.
92. Vidal-Russell, R. and D. L. Nickrent. 2008. The first mistletoes: origins of aerial parasitism in Santalales. Molecular Phylogenetics and Evolution 47 (2): 523-537. For a PDF file of this article (constructed from original files, not MPE pdf that is restricted by Elsevier), click HERE.
91. Der, J. P. and Nickrent, D. L. 2008. A molecular phylogeny of Santalaceae (Santalales). Systematic Botany 33: 107-116. For a PDF file of this article, click HERE.
90. Malécot, V. and Nickrent, D. L. 2008. Molecular phylogenetic relationships of Olacaceae and related Santalales. Systematic Botany 33: 97-106. For a PDF file of this article, click HERE.
75. Malécot, V., D. L. Nickrent, P. Baas, L. van den Oever, D. Lobreau-Callen. 2004. Phylogeny of Olacaceae based on a morphological cladistic analysis. Systematic Botany. 29:569-586. For a PDF file of this article, click HERE
60. Nickrent, D. L., and V. Malécot. 2001. A molecular phylogeny of Santalales. Pages 69-74 in A. Fer, P. Thalouarn, D. M. Joel, L. J. Musselman, C. Parker, and J. A. C. Verkleij, eds. Proceedings of the 7th. International Parasitic Weed Symposium. Faculté des Sciences, Université de Nantes, Nantes, France. For a PDF file of this article, click HERE. An updated web version of this work is HERE.
39. Nickrent, D. L. and R. J. Duff. 1996. Molecular studies of parasitic plants using ribosomal RNA. Pp. 28-52. In: M. T. Moreno, J. I. Cubero, D. Berner, D. Joel, L. J. Musselman, C. Parker (eds.), Advances in Parasitic Plant Research, Junta de Andalucia, Dirección General de Investigación Agraria, Cordoba, Spain. For PDF file of this article, click HERE.
20. Nickrent, D. L. and C. R. Franchina. 1990. Phylogenetic relationships of the Santalales and relatives. Journal of Molecular Evolution 31: 294-301. For a PDF file of the article, click HERE.

7. Phylogenetics and species relationships among mistletoes (Loranthaceae, Viscaceae, Misodendraceae)

Arceuthobium AJB cover

Tristerix AJB cover
Some of my first work in the early days following the application of PCR involved generating a molecular phylogeny of species in Arceuthobium (Viscaceae) using nuclear ribosomal internal transcribed spacer (ITS) sequences (Nickrent et al. 1994).  A later collaborative study generated a phylogeny of all species of Arceuthobium, using both ITS and a chloroplast spacer sequences (Nickrent et al. 2004). This work showed how different conclusions can be reached when classifications are based upon morphological vs. molecular characters.  For diminutive parasites such as A. pusillum (first journal cover, to the left) and A. douglasii, morphological convergence can lead to erroneous classifications that is only detected using genetic markers.  We also showed that many of the mistletoe pathogens from the western U.S. related to A. campylopodum are so closely related they could be considered one biological species.  

While still a graduate student, Guille Amico began investigating fruit dispersal in Tristerix (Loranthaceae).  When he came to SIUC he began collecting molecular data to investigate genetic differentiation in this mistletoe. Using a combined nuclear ITS and chloroplast spacer dataset, he generated a molecular phylogeny for all but one species of Tristerix.  This analysis showed Tristerix to be composed of a northern clade (six species) and a southern clade (four species), suggesting an alternate subgeneric classification. Speciation appeared to be correlated with the emergence of the matorral and cloud forest biomes and was driven by interactions with pollinators and seed dispersers. Tristerix aphyllus was sister to T. corymbosus of the matorral, not to neighboring temperate forest populations, thus rendering the latter species paraphyletic. This represents a case of ecological sympatric speciation.  The paper was published in American Journal of Botany (Amico et al. 2007) and the cover featured T. penduliflorus (left). 

The population genetics of these two Tristerix species was further investigated in the study by Amico et al. (2009).  And Guille's appetite for understanding the phylogenetic and biogeographic relationships of South American loranths was still not satisfied!  He continued with a studies of Ligaria cuneifolia and the genus Tripodanthus, the latter of which contains widely disjunct populations.

Not be outdone by her husbands energy and motivation, Romina Vidal-Russell, added another project to her already time-consuming work on loranths.  She generated a molecular phylogeny of Misodendron (Misodendraceae), a mistletoe parasitic on Nothofagus, the southern hemisphere beech.  The paper in Systematic Botany in 2007 reported results from a molecular phylogenetic analysis (chloroplast spacers) and morphological characters.

Publications:

120. Pelser, P. B., D. L. Nickrent, A. R. T. Reintar, & J. F. Barcelona. 2016. Lepeostegeres cebuensis (Loranthaceae), a new mistletoe species from Cebu, Philippines. Phytotaxa 266(1):48-52. For a PDF file of this article click HERE.
113. Amico, G. C., R. Vidal-Russell, M. A. Aizen, and D. L. Nickrent. 2014. Genetic diversity and population structure of the mistletoe Tristerix corymbosus (Loranthaceae). Plant Systematics and Evolution 300:153-162.  For a PDF file of this article, click HERE.
109. D. L. Nickrent. 2012. Justification for subspecies in Arceuthobium campylopodum (Viscaceae). Phytoneuron 51: 1-11.
For a PDF file of this article click HERE or visit website HERE.
108. Amico, G. C., Romina Vidal-Russell, R., Garcia, M. A.and Nickrent, D. L. Evolutionary history of the South American mistletoe Tripodanthus (Loranthaceae) using nuclear and chloroplast markers. Syst. Bot. 37: 218-225. For a PDF file of this article, click HERE.
99. Amico, G. C. and D. L. Nickrent. 2009. Population structure and phylogeography of the mistletoes Tristerix corymbosus and T. aphyllus (Loranthaceae) using chloroplast DNA sequence variation. American Journal of Botany 96: 1571-1580.
For a PDF file of this article click HERE.
86. Amico, G. C., R. Vidal-Russell and D. L. Nickrent. 2007. Phylogenetic relationships and ecological speciation in the mistletoe Tristerix (Loranthaceae): the influence of pollinators, dispersers, and hosts.  American Journal of Botany 94: 558-567. For a PDF file of this article, click HERE. Supplementary data HERE.  For a Spanish version of this paper (Capítulo II, Filogenia del Género Tristerix - from G. Amico's Ph.D. dissertation), click HERE.
87. Vidal-Russell, R. and D. L. Nickrent. 2007. A molecular phylogeny of the feathery mistletoe Misodendrum. Systematic Botany 32:560-568. For a PDF file of this article, click HERE.
83. Amico, G. C. and D. L. Nickrent.  2007. Phylogeography of the Argentine mistletoe, Ligaria cuneifolia (Loranthaceae). Darwiniana 45(S): 63-64. For a PDF file of the article, click HERE.
82. Amico, G. C. and D. L. Nickrent. 2007. A molecular phylogeny of the mistletoe genus Tripodanthus (Loranthaceae). Darwiniana 45(S): 61-63. For a PDF file of the article, click HERE.
69. Nickrent, D. L., M. A. García, M. P. Martín, and R. L. Mathiasen. 2004. A phylogeny of all species of Arceuthobium (Viscaceae) using nuclear and chloroplast DNA sequences. American Journal of Botany. 91:125-138. For a PDF file of this article, click HERE.
54. Nickrent, D. L. 2000. Mistletoe phylogenetics: Current relationships gained from analysis of DNA sequences. Pp. 48-57 in: Proceedings of the 48th. Annual Western International Forest Disease Work Conference, August 14-18, Kona, Hawai'i. For a PDF file of this article, click HERE.
40. Nickrent, D. L. 1996. Molecular Systematics of Arceuthobium. Chapter 15, Pp. 155-170 In: F. G. Hawksworth and D. Wiens (eds.), Dwarf Mistletoes: Biology, Pathology and Systematics. USDA Forest Service Agricultural Handbook 709, Washington DC. This entire work is available online; click HERE.
36. Nickrent, D. L. 1995. Molecular systematics of Arceuthobium. Pages 74-81. Proceedings of the 43rd Western International Forest Disease Work Conference, Whitefish, Montana.
34. Nickrent, D. L., K. P. Schuette, and E. M. Starr. 1994. A molecular phylogeny of Arceuthobium (Visaceae) based on nuclear ribosomal DNA internal transcribed spacer sequences. American Journal of Botany 81:1149-1160. For a PDF file of the article, click HERE.

8. Parasitic plant plastome evolution

Pilostyles 16S

Cynomorium coccineum

Very small plastomes can be seen from the sequenced or restriction mapped plastomes of Epifagus (70 kb), the euglenoid Astasia longa (73 kb), Conopholis (Orobanchaceae, ca. 43 kb), and Cytinus (Cytinaceae, possibly 20 kb). This trend begs the question “can the plastome be lost?” as has apparently occurred with mitochondria resulting in hydroxysomes. The presence of small-subunit rRNA (16S) sequences in practically all haustorial parasite lineages indicated that this evolutionary reduction has not gone to completion (Nickrent et al. 1997a). 

To date, most information on holoparasite plastomes comes from the study of higher-order small-subunit (16S) rRNAs, and these were generated from representatives of the following families: Apodanthaceae, Cynomoriaceae, Cytinaceae, Balanophoraceae, Hydnoraceae, and Mitrastemonaceae.  In general, plastid 16S rRNAs are extremely conservative among all land plants.  For example, most pairwise comparisons among angiosperms differ by 2-3% in substitutions. But these holoparasites show an increasingly greater number of mutations from 7.3% in Cynomorium to 35.9% in Corynaea.  Despite this high mutation levels, 16S structures constructed for all species except Pilostyles possess the typical complement of 50 helices thereby providing indirect evidence supporting their functionality.  The trend toward increasing numbers of base substitutions in the holoparasites is accompanied by a marked increase in A+U content of the rRNA which we termed the "A/T drift" phenomenon. This is especially apparent in Corynaea whose SSU rDNA sequence is 72% A+T.   The Nickrent et al. (1997a) publication showed that Pilostyles had the most unusual molecule ever seen in plants. Evidence that this RNA actually exists in the cells from RT-PCR experiments reported in the 1997 publication and later from the EST library from this plant (see above). But the genus Pilostyles has an amazing geographical distribution, with species in North, Central and South America, the Middle East, and western Australia.  Steven Wylie struck up a collaboration because his group was working on P. hamiltonii and wanted to know if the same bizarre plastid rRNAs were present in this species.  As it turned out, yes, these molecules were also highly modified, but in different places than the N. American P. thurberi.  Stayed tuned for the paper that hopefully will be published soon in Plant Molecular Biology.

In 2004 Miguel A. García and I published a paper on the plastid large subunit (26S) rDNA of the holoparasite Cynomorium (Cynomoriaceae, shown at left).  Instead of all the plastomes containing identical 26S sequences within the plant (as is the case for essentially all previously studied plants), Cynomorium contained numerous different copies, a phenomenon called heteroplasmy.  To put this in context, the degree of difference between the 26S rDNA clones from Cynomorium exceeds the difference seen among all land plants taken together.  This work continues to challenge previous concepts about the organization and function of plastomes in plants.

In 2009 Miguel and I published another paper, this one on the evolution of the plastome in Arceuthobium. Dwarf mistletoes are an interesting case study because despite gaining much carbon from their host, they must retain photosynthesis for the seedling stage of their life cycle.  Thus, studying the modifications in their plastome documents the range and limit of mutational change in plants approaching holoparasitism.


Publications:

In review. Nickrent, D. L., R. R. Gutell, J. C. Lee, L. M. Maccarone, P. Hollick, J. McComb, S. J. Wylie. 2012. Diversity and evolution of plastid small-subunit rRNA: Higher order structures in Pilostyles (Apodanthaceae). Plant Molecular Biology.
98. Nickrent, D. L. and M. A. García. 2009. On the brink of holoparasitism: plastome evolution in dwarf mistletoes (Arceuthobium, Viscaceae). Journal of Molecular Evolution 68: 603-615. For a PDF file of this article click HERE.
70. García, M. A., E. H. Nicholson, and D. L. Nickrent. 2004. Extensive intra-individual variation in plastid rDNA sequences from the holoparasite Cynomorium coccineum (Cynomoriaceae). Journal of Molecular Evolution. 58: 1-11. For a PDF file of this article, click HERE.
44. Nickrent, D. L., Y. Ouyang, R. J. Duff, and C. W. dePamphilis. 1997b. Do nonasterid holoparasitic flowering plants have plastid genomes? Plant Molecular Biology 34: 731-743.For a PDF file of this article, click HERE.
43. Nickrent, D. L., Duff, R. J. and Konings, D. A. M. 1997a. Structural analyses of plastid-derived 16S rRNAs of holoparasitic angiosperms. Plant Molecular Biology 34: 717-729. For a PDF file of this article, click HERE.

9. Phylogenetic, taxonomic, and molecular evolutionary studies of holoparasites

Rafflesia Science cover Classification of these nonphotosynthetic plants using traditional means has been difficult owing to morphological reductions and losses. Determining evolutionary relationships within and among these holoparasites is arguably the most challenging task facing those wishing to reconstruct angiosperm phylogenies.  Why so difficult? As shown by our early work with nuclear 18S rRNA, these plants have very high substitution rates for most genes.  Moreover, their plastomes are highly modified and genes typically used in phylogenetics (e.g. rbcL) are missing. Our strategy has been to use more conservative mitochondrial genes (e.g. atp1 and matR) and to use model-based phylogenetic reconstruction methods (instead of maximum parsimony) to avoid long-branch attraction artifacts.  These molecular methods have paid off in that now all holoparasite lineages have been placed within the global angiosperm phylogeny.  Examples of these studies are:
  • placement of Hydnoraceae, which contains just two genera, Prosopanche (South and central America) and Hydnora (Africa/Madagascar), within Piperales, the order of the black pepper plant.
  • molecular phylogenetic analyses placed the holoparasites of Balanophoraceae in Santalales, an otherwise entirely hemiparasitic order. This position has been confirmed by separate gene sequences generated in the lab of Jer-Ming Hu, but to date we still don't know the exact placement within the order.
  • Molecular phylogenetic work on Balanophoraceae and Cynomorium (Nickrent et al. 2005) cleared up a number of taxonomic issues.  This work showed that Cynomorium is not related to Balanophoraceae but to Saxifragales, the order with Sedum or stonecrops. 
  • The phylogeny of Rafflesiaceae s. lat. has been very challenging owing not only to rate increases but also to horizontal gene transfer.  Four groups were traditionally recognized based on morphology: 1) Cytinus and Bdallophyton (Cytinaceae), 2) Rafflesia, Rhizanthes, and Sapria (Rafflesiaceae in the strict sense), 3) Apodanthes, Pilostyles, and Berlinianche (Apodanthaceae), and 4) Mitrastema (Mitrastemonaceae).  Results of phylogenetic analyses from my lab and collaborators (Nickrent et al. 2004) showed that these four groups represented four independent clades: 1) Malvales, 2) Malphighiales, 3) Cucurbitales and 4) Ericales.
  • In a collaborative project (Davis et al. 2007) we generated additional sequences that allowed us to place Rafflesiaceae more specifically in Malpighiales.  This work showed that Rafflesiaceae is closely related to Euphorbiaceae, a surprising result because flowers in Euphorbiaceae are very small vs. very large in Rafflesia.
  • A more detailed phylogenetic study of Malvales showed that Cytinaceae (Cytinus in the Old World, Bdallophyton in the New World) are most closely related to the New World Muntingiaceae (Nickrent 2007).
Publications:

102. Govaerts, R. and D. L. Nickrent. 2010. Cytinus ruber (Cytinaceae). Curtis’s Botanical Magazine 26: 314-321. For a PDF file of this article click HERE.
88. Nickrent, D. L. 2007. Cytinaceae are sister to Muntingiaceae (Malvales). Taxon 56: 1129-1135. For a PDF file of this article, click HERE.
84. Davis, C. C., M. Latvis, D. L. Nickrent, K. J. Wurdack, D. A. Baum. 2007. Floral gigantism in Rafflesiaceae.  Science 315: 1812. For a PDF file of this article, click HERE.  Supplementary data HERE.
79. Nickrent, D. L., J. P. Der, and F. E. Anderson. 2005. Discovery of the photosynthetic relatives of the "Maltese mushroom" Cynomorium. BMC Evolutionary Biology 5:38. For a PDF file of this article, click HERE. For the full text online version, go HERE.
76. Nickrent, D. L, A. Blarer, Y.-L. Qiu, R. Vidal-Russell, F. E. Anderson. 2004. Phylogenetic inference in Rafflesiales: the influence of rate heterogeneity and horizontal gene transfer. BMC Evolutionary Biology 4: 40. For a PDF file of this article, click HERE (1.2 MB). For the full text online version, go HERE.
65. Nickrent, D. L., A. Blarer, Y.-L. Qiu, D. E. Soltis, P. S. Soltis, and M. Zanis. 2002. Molecular data place Hydnoraceae with Aristolochiaceae. Amer. J. Bot. 89 (11): 1809-1817. For a PDF file of this article, click HERE.
45. Duff, R. J. and D. L. Nickrent. 1997. Characterization of mitochondrial small-subunit ribosomal RNAs from holoparasitic plants. Journal of Molecular Evolution 45:631-639. For a PDF file of this article, click HERE.
32. Nickrent, D. L. and E. M. Starr. 1994. High rates of nucleotide substitution in nuclear small-subunit (18S) rDNA from holoparasitic flowering plants. Journal of Molecular Evolution 39:62-70. For a PDF file of article, click HERE.

10. Morphological, developmental and evolutionary studies in parasitic plants

Striga autogamy

Balanophora female flowers
Some of the first research I conducted as a new recruit to parasitic plants was with Lytton Musselman on Striga.  Using sectioned flower buds, we showed that the witchweed Striga asiatica undergoes self-pollination (autogamy, shown to the left), which indicates it can readily colonize new areas by dispersing very few seeds.  Flowers are central to understanding angiosperm systematics and phylogeny, hence I have studied them throughout my career. I feel fortunate to have been involved as a collaborator on three projects involving floral morphology:
  • The first, with Albert Blarer and Peter Endress, looked at floral morphology and anatomy in all three genera of Apodanthaceae: Apodanthes, Berlinianche, and Pilostyles (Blarer et al. 2004 in Plant Systematics and Evolution).
  • The next collaboration followed from the dissertation research by Roland Eberwein who worked with Anton Weber (Austria).  This developmental study used scanning electron microscopy to document the ontogeny of flowers in Balanophora. The female flowers in this genus are the smallest among angiosperms, reduced to just a few dozen cells (shown at left).  This work was published in the American Journal of Botany in 2009.
  • Ryan Brown's evolution-development study of ovules took place in Chuck Gasser's lab (UC Davis).  In Santalales, there is an ovule reduction series from bitegmic (two integuments), to unitegmic (one) to ategmic (no integuments).  We used orthologs to the ANT and BEL1 genes in Arabidopsis to study the expression in representative Santalales (Comandra, Santalum, and Phoradendron). These genes were found to be expressed on unitegmic ovules and the surface of ategmic ones, thus suggesting that integument loss actually involves fusion of tissues. This work was published in Evolution and Development in 2010.
Publications:

100. Brown, R. H., D. L. Nickrent, and C. S. Gasser. 2010. Expression of ovule and integument-associated genes in reduced ovules of Santalales. Evolution and Development 12: 229-238. For a PDF file of this article click HERE.
97. Eberwein, R., D. L. Nickrent, and A. Weber. 2009. Development and morphology of flowers and inflorescences in Balanophora papuana and B. elongata (Balanophoraceae). American Journal of Botany 96: 055-1067.
For a PDF file of this article click HERE.
71. Blarer, A., D. L. Nickrent, and P. K. Endress. 2004. Comparative floral structure and systematics in Apodanthaceae (Rafflesiales). Plant Systematics and Evolution. For a PDF file of this article, click HERE.
4. Nickrent, D. L., L. J. Musselman, J. L. Riopel, and R. E. Eplee. 1979. Haustorial initiation and non-host penetration in witchweed (Striga asiatica). Ann Bot. 43: 233-236. For a PDF file of the article, click HERE.
3. Nickrent, D. L. and L. J. Musselman. 1979. Autogamy in the American strain of witchweed, Striga asiatica (Scrophulariaceae). Brittonia 31:253-256. For a PDF file of the article, click HERE.

11.  Local flora populational and floristic studies


Dalea purpurea

Andropogon gerardii
In addition to molecular phylogenetic studies, my students and collaborators have engaged in studies centering around the population biology of native North American plants. Indeed, my very first publication resulted from work I conducted when I was an undergraduate at Old Dominion University working with Lytton Musselman on the flora of the Great Dismal Swamp.  

Isozyme analyses of mistletoes led me towards applying this methodology to questions in other groups.  For example, genetic diversity in Mead's Milkweed was assessed using isozymes in a collaborative project between Diane Tecic (SIUC graduate student) and Marlin Bowles (Morton Arboretum).  Asclepias meadii is a federal threatened milkweed that was once more common in the prairies of the Midwest.  The few remaining small populations in Illinois, Iowa, and northern Missouri persist vegetatively but no longer produce seeds and are vulnerable to stochastic extinction processes.  Isozyme electrophoresis was used to measure the amount and distribution of genetic variation in A. meadii and to provide guidance for its recovery and restoration (Tecic et al. 1998). The data indicate that the introduction of additional genotypes into declining populations is necessary.  These data, and results of artificial crosses made by M. Bowles with geographically distant sources, show that outbreeding depression is less a concern than previously thought, at least for these plants. 

Another isozyme study conducted on two rare Illinois legumes (Dalea foliosa and Astragalus tennesseenis) was begun by a graduate student (Bethany Wiltshire) in my lab in 1994.  This work was “resurrected” by Dr. Adrienne Edwards at the Illinois Natural History Survey who helped collect additional data and conduct more analyses.  These data were published in the Journal of the Torrey Botanical Society (Edwards et al. 2004). 

My lab has also applied DNA methods to plant population genetic questions.  Although many studies focus on rare and endangered plants, a former graduate student in the Nickrent lab (Danny Gustafson) was interested in characterizing the genetic diversity and genetic identity of species that are dominants in the Illinois tallgrass prairie.  RAPD (randomly amplified polymorphic DNA) as well as isozyme data were collected for Andropogon gerardii, Sorghastrum nutans, and Dalea purpurea populations from remnant and restored Illinois tallgrass prairies, Konza Prairie Research Natural Area (Kansas), and several commercially available cultivars of A. gerardii and S. nutans.  This work has shown that 1) there are genetic difference between local and non-local seed sources, 2) it is not correct to assume that small remnant populations have low genetic diversity relative to larger populations, and 3) there are differences in plant performance between local and non-local A. gerardii, S. nutans, and D. purpurea seed sources.  Results from Gustafson’s dissertation research have been published in several research journals (Gustafson et al. 1999, 2001, 2002, 2004a, b).
Publications:

78. Gustafson, D. J., Gibson, D. J., and D. L. Nickrent. 2005. Using local seeds in prairie restoration-data supports the paradigm. Native Plants Journal 6:25-28.
77. Edwards, A. L., B. Wiltshire and D. L. Nickrent. 2004. Genetic diversity in Astragalus tennesseensis and the federal endangered Dalea foliosa (Fabaceae). Journal of the Torrey Botanical Society. 131: 279-291.
For a PDF file of this article, click HERE.
74. Gustafson, D. J., D. J. Gibson and D. L. Nickrent. 2004. Competitive relationships of Andropogon gerardii (big bluestem) from remnant and restored native populations and select cultivated varieties. Functional Ecology 18: 451-457.For a PDF file of this article, click HERE
73. Gustafson, D. J., D. J. Gibson and D. L. Nickrent. 2004. Conservation genetics of two co-dominant grass species in the endangered grassland ecosystem. Journal of Applied Ecology 41: 389-397.
For a PDF file of this article, click HERE.
64. Gustafson, D. J., D. J. Gibson, D. L. Nickrent. 2002. Genetic diversity and competitive abilities of Dalea purpurea (Fabaceae) from remnant and restored grasslands. Int. J. Plant Sci. 163 (6):979-990. For a PDF file of this article, click HERE.
62. Gustafson, D. J., D. J. Gibson, and D. L. Nickrent. 2001. Characterizing three restored Andropogon gerardii Vitman (big bluestem) populations established with Illinois and Nebraska seed: established plants and their offspring, pp. 118-124, In Proceedings of the 17th North American Prairie Conference. Seeds for the Furture; Roots of the Past. Neil Bernstein and Laura J. Ostrander (eds.). Northern Iowa Area Community College, Mason City, Iowa.
53. Gustafson, D. J., D. J. Gibson, and D. L. Nickrent. 1999. Random amplified polymorphic DNA variation among remnant big bluestem (Andropogon gerardii Vitman) populations from Arkansas' Grand Prairie. Molecular Ecology 8: 1693-1701. For a PDF file of this article, click HERE.
47. Tecic, D. L., J. McBride, M. L. Bowles and D. L. Nickrent. 1998. Genetic variability in the federal threatened Mead's milkweed (Asclepiadaceae: Asclepias meadii Torrey) determined by allozyme electrophoresis. Annals of the Missouri Botanical Garden 85:97-109. For a PDF file of this article, click HERE.
31. Pavlik, B. M., D. L. Nickrent, and A. M. Howald. 1993. The recovery of an endangered plant. I. Creating a new population of Amsinckia grandiflora. Conservation Biology 7:510-526.
For a PDF file of the article, click HERE.
11. Nickrent, D. L., W. H. Eshbaugh, and T. K. Wilson. 1988. The vascular flora of Andros Island, Bahamas. Kendall/Hunt Publishing Co., Dubuque, Iowa. 185 pp. ISBN 0-8403-4756-1. For a PDF file of this book, click HERE (5.8 MB).
2. Nickrent, D. L., L. J. Musselman, L. A. Pitchford, and D. W. Sampson. 1978. The distribution and ecology of Dryopteris in southeastern Virginia and adjacent North Carolina. Amer. Fern J. 68:45-51.
1. Musselman, L. J., D. L. Nickrent, and G. F. Levy. 1977. A contribution towards a vascular flora of the Great Dismal Swamp. Rhodora 79:240-268.



12.  Land plant phylogenetic studies

Phaeoceros 19S rRNA Phylogenetic relationships among embryophytes (tracheophytes, mosses, liverworts, and hornworts) have long intrigued botanists and, with the dawn of the molecular era, tool became available to address deep evolutionary relationships among the various groups.  Through pure serendipity, my postdoc at the time, Dr. R. Joel Duff, accidentally PCR amplified and sequenced a mitochondrial small-subunit (SSU) rDNA, not plastid rDNA. We then realized that very few of these rRNA sequences existed for parasitic plants or land plants in general.  This began our investigations of the utility of this gene for phylogenetic reconstruction of deep clades within land plants.

The publication in American Journal of Botany (Duff and Nickrent 1999) was the first demonstration of the utility of this gene for assessing phylogenetic relationships among plants. A higher-order structure of mitochondrial SSU rRNA from the hornwort Phaeoceros is shown to the left. The phylogenetic trees showed strong support for the majority of higher-level land plant clades, such as hornworts, liverworts, mosses, lycopsids, leptosporangiate and eusporangiate ferns, gymnosperms and angiosperms.  Support for a sister relationship between Equisetum and leptosporangiate ferns and a monophyletic gymnosperm clade that was sister to angiosperms were also demonstrated – two relationships later confirmed by workers using other genes.  Mitochondrial SSU rDNA sequences were used in combination with other genes in a collaborative study published in the the journal Molecular Biology and Evolution (Nickrent et al. 2000).
Publications:

56. Nickrent , D. L., C. L. Parkinson, J. D. Palmer, and R. J. Duff. 2000. Multigene phylogeny of land plants with special reference to bryophytes and the earliest land plants. Molecular Biology and Evolution: 17: 1885-1895. For a PDF file of this article, click HERE.
55. Renzaglia, K. S., R. J. Duff, D. L. Nickrent, and D. J. Garbary. 2000. Vegetative and reproductive innovations of early land plants: implications for a unified phylogeny. Philosophical Transactions of the Royal Society of London 355: 769-793.
For a PDF file of this article, click HERE. Note: file size 2.6 mb.
52. Soltis, P. S., D. E. Soltis, P. G. Wolf, D. L. Nickrent, S.-M. Chaw, and R. L. Chapman. 1999. The phylogeny of land plants inferred from 18S rDNA sequences: pushing the limits of rDNA signal? Mol. Biol. Evol. 16: 1774-1784. For a PDF file of this article, click HERE.
51. Duff, R. J. and D. L. Nickrent. 1999. Phylogenetic relationships of land plants using mitochondrial small-subunit rDNA sequences. American Journal of Botany 86:372-386.  
For a PDF file of this article, click HERE.


13.  Angiosperm phylogeny

angiosperm 18S tree During the course of sequencing 18S rDNA among members of Santalales, it became apparent that additional “outgroup” taxa would be required to address the position of this order among all angiosperms.  In 1993, Mark Chase and a number of collaborators published an extensive molecular phylogenetic study of angiosperms using over 200 sequences of the chloroplast-encoded gene rbcL. To investigate the phylogenetic utility of 18S rDNA sequences, I conducted preliminary analyses using the same suite of species for both genes.  A collaboration was then started with Doug Soltis who contributed additional sequences.  The results of those analyses were published in the Annals of the Missouri Botanical Garden (Nickrent and Soltis 1995).

The 1995 paper helped dispel the widely-held view that 18S rDNA contained too few nucleotide substitutions to address phylogenetic relationships among angiosperms.  Doug and Pam Soltis, and a number of collaborators, extended this work by conducting a large-scale sequencing study (Soltis et al. 1997) that used over 200 angiosperm 18S sequences.  This work showed that the 18S rDNA and rbcL topologies were highly congruent.  Previous difficulties using this gene were because they were based on too few sequences and sequences with large numbers of errors. 18S rDNA was used in the multigene analysis of hundreds of angiosperms by Soltis et al. (2000) and this tree formed the basis for reclassification of flowering plants by the APG group (1998, 2003, 2009).
Publications:

49. APG. 1998. An ordinal classification for the families of flowering plants. Annals of the Missouri Botanical Garden. 85: 531-553 [APG= The Angiosperm Phylogeny Group, compiled by K. Bremer, M. W. Chase, and P. F. Stevens, plus 26 other authors]. For the complete paper, visit the web site HERE.
42. Soltis, D. E., P. S. Soltis, D. L. Nickrent, L. A. Johnson, W. J. Hahn, S. B. Hoot, J. A. Sweere, R. K. Kuzoff, K. A. Kron, M. W. Chase, S. M. Swensen, E. A. Zimmer, S.-M. Chaw, L. J. Gillespie, J. W. Kress and K. J. Sytsma. 1997. Angiosperm phylogeny inferred from 18S ribosomal DNA sequences. Annals of the Missouri Botanical Garden 84:1-49.
For a PDF file of the article, click HERE.
37. Nickrent, D. L. and D. E. Soltis. 1995. A comparison of angiosperm phylogenies based upon complete 18S rDNA and rbcL sequences. Annals of the Missouri Botanical Garden 82:208-234. For a PDF file of article, click HERE.


14.  Review articles, methodology - various topics

Plantas Parasitas Amphorogynaceae tree Mistletoes Plant Disease Molecular Systematics Plants II
Publications:

106. Nickrent, D. L. 2011. Santalales (Including Mistletoes). Encyclopedia of Life Science. John Wiley & Sons, Ltd.: Chichester [DOI: 10.1002/9780470015902.a0003714.pub2]. Wiley website (search for article) HERE. For a PDF file of this article click HERE.
94. Mathiasen, R. M., D. L. Nickrent, D. C. Shaw, and D. M. Watson. 2008. Mistletoes: pathology, systematics, ecology, and management. Plant Disease 92 (7): 988-1006. For a PDF file of this article click HERE.
89. Nickrent, D. L. 2008. Parasitic Plants. Pp. 251-253 in McGraw-Hill Yearbook of Science & Technology. For a PDF file of this article, click HERE.
72. Nickrent, D. L. and L. J. Musselman. 2004. Parasitic flowering plants. American Phytopathological Society APSnet Education Center, the Plant Health Instructor web publication [HERE]. The Plant Health Instructor. DOI: 10.1094/PHI-I-2004-0330-01.

67. Nickrent, D. L. 2002. Orígenes filogenéticos de las plantas parásitas. Capitulo 3, pp. 29-56 In J. A. López-Sáez, P. Catalán and L. Sáez [eds.], Plantas Parásitas de la Península Ibérica e Islas Baleares. Mundi-Prensa Libros, S. A., Madrid. [Phylogenetic Origins of Parasitic Plants. Chapter 3, pp. 29-56, Parasitic Plants of the Iberian Peninsula and Balearic Islands.
English translation, click HERE.
66. Nickrent, D. L. 2002. Plantas parásitas en el mundo. Capitulo 2, pp. 7-27 In J. A. López-Sáez, P. Catalán and L. Sáez [eds.], Plantas Parásitas de la Península Ibérica e Islas Baleares. Mundi-Prensa Libros, S. A., Madrid. [Parasitic Plants of the World. Chapter 2, pp. 7-27, Parasitic Plants of the Iberian Peninsula and Balearic Islands. English translation, click HERE.
59. Nickrent, D. L. 2001. Parasitic Plants. In: Plant Sciences for Students, Vol. 3 (0-02-865432-3), R. Robinson (ed.), Gale Group (part of Macmillan Reference), Farmington Hills, MI. Pages 110-112.
58. Nickrent, D. L. 2001. Santalales (Mistletoe). Treatment A3714 in Encyclopedia of Life Sciences, Macmillan Publishers Ltd. (August 2001). For a PDF file of this article, click HERE.
50. Nickrent, D. L., R. J. Duff, A. E. Colwell, A. D. Wolfe, N. D. Young, K. E. Steiner, and C. W. dePamphilis. 1998. Molecular Phylogenetic and Evolutionary Studies of Parasitic Plants. Pp. 211-241 (Chapter 8) In: Molecular Systematics of Plants II. DNA Sequencing. D. Soltis, P. Soltis, J. Doyle (eds.). Kluwer Academic Publishers, Boston, MA. For a PDF file of this article, click HERE. Note: file is 10.9 mb in size.
41. Nickrent, D. L. 1997. Review of "Parasitic Plants," M. C. Press and J. D. Graves (editors), Chapman and Hall, Ecology 78:1612-1613.
39. Nickrent, D. L. and R. J. Duff. 1996. Molecular studies of parasitic plants using ribosomal RNA. Pp. 28-52. In: M. T. Moreno, J. I. Cubero, D. Berner, D. Joel, L. J. Musselman, C. Parker (eds.), Advances in Parasitic Plant Research, Junta de Andalucia, Dirección General de Investigación Agraria, Cordoba, Spain. For a MSWord file of this article, click HERE (better resolution on the figures than the PDF). For a PDF file of this article, click HERE.
33. Nickrent, D. L. 1994. From field to film: Rapid sequencing methods for field collected plant species. BioTechniques 16: 470-475. For a PDF file of article, click HERE.


15.  Isozymes - various topics and taxonomic groups

isozyme gels The list of publications below spans the time frame from when I was a graduate student at Miami University (Oxford, OH) to an Assistant Professor at the University of Illinois Urbana-Champaign to my early years at SIUC.  During this time, isozyme electrophoresis was the major methodology I employed to examine population structure and interspecific relationships in plants.  My work with isozymes began with Arceuthobium but expanded to include other plants such as Dedeckera (Polygonaceae), Asclepias (Apocynaceae), and even fungi (via collaborations).  About the time I moved to SIUC (1990), I began to transition from isozymes to DNA-based methodologies, mainly because of the advent of PCR.  My student Beth Wiltshire used isozymes to examine genetic diversity in two rare legumes, Dalea foliosa and Astragalus tennesseensis.  This work was unpublished until Adrienne Edwards added to the data and conducted additional analyses (Edwards et al. 2004).

Another of my graduate students, Danny Gustafson conducted isozyme analysis (as well as RAPDs) on several prairie plants, Andropogon gerardii, Sorghastrum nutans (both Poaceae) and Dalea purpurea (Fabaceae).  Although now somewhat displaced by DNA-based methods such as microsatellites, isozymes were the method of choice up to the 1990s and are still used today.  An example is the recent paper by Wiens et al. (2012, Biol. J. Linn. Soc. 105:269-292) that looked at genetic diversity in Adenostoma (Rosaceae) and documented a phenomenon we first reported in Dedeckera in 1989!
Publications:

77. Edwards, A. L., B. Wiltshire and D. L. Nickrent. 2004. Genetic diversity in Astragalus tennesseensis and the federal endangered Dalea foliosa (Fabaceae). Journal of the Torrey Botanical Society. 131: 279-291. For a PDF file of this article, click HERE.
 47. Tecic, D. L., J. McBride, M. L. Bowles and D. L. Nickrent. 1998. Genetic variability in the federal threatened Mead's milkweed (Asclepiadaceae: Asclepias meadii Torrey) determined by allozyme electrophoresis. Annals of the Missouri Botanical Garden 85:97-109. For a PDF file of this article, click HERE.
30. Simcox, K. D., W. L. Pedersen, and D. L. Nickrent. 1993. Isozyme diversity in Septosphaeria turcica. Canadian Journal of Plant Pathology 15:91-96. For a PDF file of the article, click HERE.
27. Hawksworth, F. G., D. Wiens, & D. L. Nickrent. 1992. New western North American taxa of Arceuthobium (Viscaceae). Novon 2: 204-211.
26. Simcox, K. D, D. L. Nickrent, and W. L. Pedersen. 1992. Comparison of isozyme polymorphism in races of Cochliobolus carbonum. Phytopathology 82:621-624.
For a PDF file of the article, click HERE.
24. Nickrent, D. L. & T. L. Butler. 1991. Biochemical systematics of the Arceuthobium campylopodum complex (dwarf mistletoes, Viscaceae). III. Genetic relationships in Arceuthobium monticola and A. siskiyouense (Viscaceae): New dwarf mistletoe species from California and Oregon. Biochemical Systematics and Ecology 19:305-313.
For a PDF file of the article, click HERE.
23. Lamboy, W. F., D. L. Nickrent, and A. G. Jones. 1991. Isozyme evidence and phenetic relationships among species in Aster section Biotia (Asteraceae). Rhodora 93:205-225.
For a PDF file of the article, click HERE.
21. Liu, Z., D. L. Nickrent, and J. B. Sinclair. 1990. Genetic relationships among isolates of Rhizoctonia solani anastomosis group 2 based on isozyme analysis. Canadian Journal of Plant Pathology. 12:336-382.
For a PDF file of the article, click HERE.
19. Nickrent, D. L. and A. L. Stell. 1990. Biochemical systematics of the Arceuthobium campylopodum complex (dwarf mistletoes, Viscaceae). II. Electrophoretic evidence for genetic differentiation in two host races of hemlock dwarf mistletoe (A. tsugense). Biochemical Systematics and Ecology 18: 267-280. For a PDF file of the article, click HERE.
18. Nickrent, D. L. and T. L. Butler. 1990. Biochemical systematics of the Arceuthobium campylopodum complex (dwarf mistletoes, Viscaceae). I. Allozymic relationships in Arceuthobium campylopodum and allies in California. Biochemical Systematics and Ecology 18:253-265.
For a PDF file of the article, click HERE.
17. Buchheim, M. A., D. L. Nickrent, and L. R. Hoffman. 1990. Systematic analysis of the Sphaeroplea (Chlorophyceae). Journal of Phycology 26:173-181.
16. Nickrent, D. L. and D. Wiens. 1989. Genetic diversity in the rare California shrub Dedeckera eurekensis (Polygonaceae). Systematic Botany 14:245-253.
For a PDF file of the article, click HERE.
15. Karalamangala, R. R. and D. L. Nickrent. 1989. An electrophoretic study of representatives of subgenus Diploxylon of Pinus. Canadian Journal of Botany 67:1750-1759.
For a PDF file of the article, click HERE.
14. Wiens, D., E. J. King, D. L. Nickrent, C. L. Calvin, and N. L. Vivrette. 1989. Embryo and seed abortion in plants. Nature 342:625-626.
For a PDF file of the article, click HERE.
13. Wiens, D., D. L. Nickrent, C. I. Davern, C. L. Calvin, and N. J. Vivrette. 1989. Developmental failure and loss of reproductive capacity in the rare palaeoendemic shrub Dedeckera eurekensis. Nature 338:65-67. For a PDF file of the article, click HERE.
10. Nickrent, D. L. 1987. Systematics and population biology of two sibling species of Arceuthobium (dwarf mistletoes, Viscaceae). Pp. 597-611 In: Proceedings of the 4th. International Symposium on Parasitic Flowering Plants, Phillipps University, Marburg, West Germany, August 2-7, 1987. Eds. H. C. Weber, W. Forstreuter.
9. Nickrent, D. L. 1986. Genetic polymorphism in the morphologically reduced dwarf mistletoes (Arceuthobium, Viscaceae): an electrophoretic study. American Journal of Botany 73:1492-1502.
For a PDF file of the article, click HERE.
8. Nickrent, D. L., S. I. Guttman, and W. H. Eshbaugh. 1984. Biosystematic and evolutionary relationships among selected taxa of Arceuthobium. Pp. 20-35 In: Proceedings of the Symposium on the Biology of Dwarf Mistletoes, Aug. 8, 1984, Technical Coordinators F. Hawksworth and R. Scharpf.
7. Nickrent, D. L. 1984. A systematic and evolutionary study of selected taxa in the genus Arceuthobium (Viscaceae). Dissertation, Miami University Department of Botany, Oxford, OH. 256 pp.